It will install many other packages for you automately, such as : ALL, CLL, pasilla, airway ,limma，DESeq2，clusterProfiler , that's why it will take a long time to finish if all of these packages are not installed before in your computer.

Then run step1 :

It always not very easy to download data if you are in China, so I also upload the file GSE42872_raw_exprSet.Rdata , you can load it directly.

Then step2:

Try to understand my codes, how did I filter the probes by the annotation of each microarry, and how I check the group information for the different samples in each experiment.

Including PCA and Cluster figures, as below:

ClusterPCA

Please ensure that you do run those codes by yourself !!!

Then step3:

Normally we will do differential expression analysis for the microarray, and LIMMA is one of the best method, so I just use it. If the expression matrix(raw counts ) comes from mRNA-seq, you can also choose DESeq based on negative binomial (NB) distributions or baySeq and EBSeq.

Once DEG finished, we can choose top N genes for heatmap as below:

heatmap

and volcano plot as below:

Last step :

Annotation for the significantly changed genes, over-representation test or GSEA for GO/KEGG/biocarta/rectome/MsigDB and so on.